pkdgrav3
September 24, 2018
http://www.pkdgrav.org/
Douglas Potter <douglas.potter@uzh.ch>
Joachim Stadel <stadel@physik.uzh.ch>
Quick Start
-----------
The pkdgrav3 code now uses the "cmake" build system. It is recommended to
use an "out of source" build. The easiest way to accomplish this is to
create a subdirectory in the pkdgrav3 source directory:
mkdir build
cd build
cmake ..
make
This will build a single executable "pkdgrav3" and other utility programs.
Prerequisites
-------------
CMake - cmake build system
Most modern systems already have cmake installed. Pkdgrav3 requires
version 3.1 or newer of cmake. You can check with "cmake --version":
pkdgrav3:~> cmake --version
cmake version 3.5.2
If you need a more recent version is can be found at:
https://cmake.org/
GSL - The GNU Scientific Library
This library is usually available on HPC systems, but if not it must be
downloaded and compiled, and can be found at this URL.
https://www.gnu.org/software/gsl/
pkdgrav3 will locate the GSL installation by invoking gsl-config, so make
sure that it is in your PATH. Alternatively, you can tell CMake where to
find it by defining GSL_ROOT_ROOT:
cmake -DGSL_ROOT_DIR=/opt/gsl/2.5
FFTW - Fast Fourier Transform Library (optional)
If FFTW is available then two advanced features are enabled in pkdgrav3.
1. Initial Condition Generation, and,
2. Power spectrum measurement
If is is not available on your system it can be obtained from:
http://www.fftw.org/
If CMake does not automatically find FFTW then you can define FFTW_ROOT_ROOT:
cmake -DFFTW_ROOT=/path/to/fftw
CUDA
If your system has a CUDA capable GPU then pkdgrav3 can use it.
The necessary toolkits can be downloaded from nVidia.
https://developer.nvidia.com/cuda-downloads
Build
-----
Once CMake has been run to produce a Makefile and associated files,
the "make" command is used to build the program, as in:
make
The build can be done in parallel so if you are on, for example,
a 16 core machine, the build process can be sped up with:
make -j 16
Running
-------
pkdgrav3
--------
This version is run using the MPI system on the cluster in question.
Normally this involves a special command (often "mpirun" or "mpiexec"),
for example:
mpiexec pkdgrav3 simfile.par
Consult your cluster documentation on how to run MPI programs.